Hyperbranched and star shaped polymers have raised tremendous interests because of their unusual structural and photochemical properties which provide them potent applications in various domains, namely ... [more ▼]

Hyperbranched and star shaped polymers have raised tremendous interests because of their unusual structural and photochemical properties which provide them potent applications in various domains, namely in the biomedical field. In this context, the development of adequate tools aiming to probe particular three-dimensional features of such polymers is of crucial importance. In this present work, ion mobility coupled with mass spectrometry was used to experimentally derive structural information related to cationized linear and star-shaped poly-ε-caprolactones as a function of their charge state and chain length. Two major conformations were observed and identified using theoretical modeling: (1) near spherical conformations whose size is invariant with the polymer topology for long and lightly charged chains and (2) elongated conformations whose size varies with the polymer topology for short and highly charged chains. These conformations were further confirmed by collisional activation experiments based on the ejection thresholds of the coordinated cations that vary according to the elongation amplitude of the polymer chains. Finally, a comparison between solution and gas-phase conformations highlights a compaction of the structure with a loss of specific chain arrangements during the ionization and desolvation steps of the electrospray process, fueling the long-time debated question related to the preservation of the analyte structure during the transfer into the mass spectrometer. [less ▲]

The threshold photoelectron spectra (TPES) of the two vicinal isomers of the 1,2-C2H2FCl molecule have been investigated in the 9-24 eV energy range using synchrotron radiation. Eight (for the cis-isomer ... [more ▼]

The threshold photoelectron spectra (TPES) of the two vicinal isomers of the 1,2-C2H2FCl molecule have been investigated in the 9-24 eV energy range using synchrotron radiation. Eight (for the cis-isomer) or nine (for the trans-isomer) bands have been observed and the corresponding ionization energies have been determined. The spectroscopic assignments are based on high level quantum chemical ab initio calculations for both isomers. Most of the observed spectral features could be interpreted. For both species the first three TPES bands exhibit a rich vibrational structure. Vibrational energies were determined and assignments were also supported by quantum chemical calculations of vibrational wavenumbers for these three ionic states of both isomers. [less ▲]

The vacuum UV photoabsorption spectrum of 1,1-C2H2FCl has been examined in detail between 5 eV and 15 eV photon energy by using synchrotron radiation dispersed by three different monochromators. Quantum ... [more ▼]

The vacuum UV photoabsorption spectrum of 1,1-C2H2FCl has been examined in detail between 5 eV and 15 eV photon energy by using synchrotron radiation dispersed by three different monochromators. Quantum chemical calculations are performed to help in the analysis of the valence/Rydberg transitions region centered at 7.05 eV including the 3a”(pi)→pi* and the 3a” (pi*)→3s Rydberg transitions. Interactions between states involving transitions to the 3s, 4d and sigma* orbitals are identified. A vibrational analysis is proposed for the structures belonging to these transitions. For the pi(3a”)→pi* transition, one vibrational progression is observed with ω3=1410±50 cm-1 and its lowest excitation energy is determined at about 6.398±0.003 eV. The pi(3a”)→3s Rydberg transition is characterized by a single progression with ω3= 1410±80 cm-1 likely starting at about 6.45 eV. These vibrations are ascribed to the C=C stretching motion. The abundant structure observed in the spectrum between 7.8 eV and 10.5 eV has been analyzed in terms of vibronic transitions to ns (δ= 0.97), np (δ= 0.63 and 0.40) and nd (δ= 0.13 and -0.11) Rydberg states which belong to series converging to the 1,1-C2H2FCl+( 2A”) ionic ground state. The analysis of the vibrational structure of the individual Rydberg states has been attempted leading to average values of the wavenumbers ω3= 1 420±20 cm-1, ω7= 720±50 cm-1 and ω9= 390±50 cm-1. Between 10.5 eV and 12.5 eV nine other Rydberg states converging to the 1,1-C2H2FCl+ ( 2A') first excited state were analyzed by the same way. The vibrational structure of these Rydberg states results from the excitation of one vibrational normal mode ν7 with an average value of ω7= 520±20 cm-1 which is assigned to the C-Cl stretching vibration as inferred from quantum chemical calculations. [less ▲]

The threshold photoelectron spectrum (TPES) of 1,1-C2H2FCl has been measured for the first time using synchrotron radiation. It has been compared to the HeI photoelectron spectrum (PES) obtained earlier ... [more ▼]

The threshold photoelectron spectrum (TPES) of 1,1-C2H2FCl has been measured for the first time using synchrotron radiation. It has been compared to the HeI photoelectron spectrum (PES) obtained earlier [Tornow G. et al., Chem.Phys. 146 115 (1990)]. Eight photoelectron bands have been observed at 10.22 eV, 12.45 eV, 13.28 eV, 14.29 eV, 14.99 eV, 17.12 eV, 17.67 eV, and at 20.23 eV successively. Only the first three bands exhibit a rich and extensive vibrational structure. Their adiabatic ionization energies are measured and a detailed vibrational analysis is presented. The assignments of the electronic bands and of the vibrational wavenumbers were made by using ab initio quantum chemical calculations. These allowed us to provide the MO description of the eight electronic states in terms of ionization and double excitation. The good correlation between predicted vibrational wavenumbers and the experimental values provides a strong basis for the assignment of all the vibrational structures. [less ▲]

The threshold photoelectron spectrum (TPES) and the constant ion state (CIS) spectra of the individual ionic states of 1,1-C2H2F2 have been recorded using synchrotron radiation. The TPES has been measured ... [more ▼]

The threshold photoelectron spectrum (TPES) and the constant ion state (CIS) spectra of the individual ionic states of 1,1-C2H2F2 have been recorded using synchrotron radiation. The TPES has been measured between 9.5 eV and 28 eV photon energy. For comparison the HeI photoelectron spectrum (HeI-PES) has also been measured and analyzed in detail. Numerous vibrational structures, reported for the first time, observed in the ground state and the seven excited states of the cation are analyzed. Quantum chemical calculations have been performed and provided support to the assignments. The exceptional contribution of autoionization to the HeI PES could be emphasized. State selected CIS spectra highlighted the importance of the autoionizing contribution to the production of almost all ionized states of 1,1-C2H2F2 observed in this work. Several peculiarities of the vibrationally resolved CIS spectra are analyzed. [less ▲]

In this paper, we investigated the inhibitory effect of mercaptophosphonate derivatives against the three subclasses of MBLs (B1, B2, and B3). All 14 tested mercaptophosphonates, with the exception of one ... [more ▼]

In this paper, we investigated the inhibitory effect of mercaptophosphonate derivatives against the three subclasses of MBLs (B1, B2, and B3). All 14 tested mercaptophosphonates, with the exception of one, behaved as competitive inhibitors for the three subclasses. <br />Apart from two compounds, all the mercaptophosphonates tested exhibit a good inhibitory effect on the subclass B2 MBL CphA with low inhibition constants (Ki<15 μM). Interestingly, compound 18 turned out to be a potent broad spectrum MBL inhibitor. <br />The crystallographic structures of the CphA-10a and CphA-18 complexes indicated that the sulfur atom of 10a and the phosphonato group of 18 interact with the Zn2þ ion, respectively. Molecular modeling studies of the interactions between two compounds and the VIM-4 (B1), CphA (B2), and FEZ-1 (B3) enzymes brought to light different binding modes depending on the enzyme and the inhibitor, consistent with the crystallographic structures. [less ▲]

in Journal of the American Society for Mass Spectrometry (2010), 21(1), 23-33

The fragmentation of the totally deuterated dinucleotide dAT(-) in labile positions (heteroatom-bound hydrogens) was compared for different MS/MS methods: CID, IRMPD, and EID. These experiments allowed us ... [more ▼]

The fragmentation of the totally deuterated dinucleotide dAT(-) in labile positions (heteroatom-bound hydrogens) was compared for different MS/MS methods: CID, IRMPD, and EID. These experiments allowed us to affirm the coexistence of several fragmentation channels. They can be classified according to the involvement of nonlabile or labile protons in the fragmentation process. Moreover, double resonance experiments were performed in IRMPD and EID. They demonstrated the existence of consecutive fragmentation processes. The probability with which each channel is taken depends on the fragmentation technique used, i.e., the energy and the time scale of the method. The fragmentation channels that involve labile protons requiring peculiar three-dimensional structures are entropically unfavorable and enthalpically favorable. They are more observed in IRMPD and EID. The involvement of labile and, therefore, exchangeable protons in the fragmentation mechanism casts doubt on the use of tandem mass spectrometry to localize incorporated deuteriums in oligonucleotides. [less ▲]

The threshold photoelectron (TPES) and the photoionization mass spectrometric (PIMS) study of CH3I in the 8-20 eV photon energy range are presented. The interpretation and assignments are supported by ab ... [more ▼]

The threshold photoelectron (TPES) and the photoionization mass spectrometric (PIMS) study of CH3I in the 8-20 eV photon energy range are presented. The interpretation and assignments are supported by ab initio calculations. The TPES shows many new discrete features in the Jahn-Teller split ground X 2E (2A'-2A”) state of CH3I+. A new continuous band starting at about 11.7 eV is detected. These observations are essentially correlated with autoionizing transitions. This interpretation is supported by constant ion state (CIS) spectroscopy. A large enhancement of the transitions to the A 2A and B 2E ionic states is ascribed to large autoionizing contributions. Based on the present calculations, the weak to very weak bands in the 18.0 eV-23.0 eV photon energy range are mainly assigned to 2a1-1 ionization and to double excitations corresponding essentially to the 2e-2 4a11 and 3a1- 1 2e-1 4a11 configurations. The photoionization mass spectrometric study allowed us to investigate in detail the ionization and dissociation of CH3I+ leading to CH2+, CH3+, I+ and CH2I+ from the threshold up to 20 eV photon energy. The experimental data are compared to ab initio calculated dissociation energies. The threshold of appearance of CH3+, I+ and CH2I+ fragments are concentrated in the 12.2-12.7 eV photon energy range. All three exit channels are correlated with the ground state of CH3I+ via nonadiabatic transitions. All three fragment ions have to appear through predissociation of the ionic X 2E state and autoionizing dissociation from the (2E3/2)6p Rydberg state. This interpretation is strongly supported by the photoabsorption spectrum measured recently in the same photon energy range [1]. At higher energies, beside direct or predissociation of the A 2A1 and B 2E states of CH3I+, autoionization is also suggested to contribute to the fragmentation in all decay channels. [less ▲]

The threshold photoelectron spectrum (TPES) and the constant ion state (CIS) spectra of the individual ionic states of C2H3F have been recorded using synchrotron radiation. For comparison a well resolved ... [more ▼]

The threshold photoelectron spectrum (TPES) and the constant ion state (CIS) spectra of the individual ionic states of C2H3F have been recorded using synchrotron radiation. For comparison a well resolved HeI photoelectron spectrum (HeI-PES) has also been measured and analyzed in detail. The TPES has been measured between 9.5 eV and 35 eV photon energy. Numerous vibrational structures, reported for the first time, observed in the ground state and the six excited states of the cation are analyzed. Quantum chemical calculations have been performed and provide strong support to the assignments. State selected CIS spectra highlighted the major importance of autoionization for the production of almost all ionized states of C2H3F observed in this work. [less ▲]

The vacuum UV photoabsorption spectrum of C2H3F has been examined in detail between 6 eV and 25 eV photon energy by using synchrotron radiation. The analysis of the data is supported by ab initio quantum ... [more ▼]

The vacuum UV photoabsorption spectrum of C2H3F has been examined in detail between 6 eV and 25 eV photon energy by using synchrotron radiation. The analysis of the data is supported by ab initio quantum mechanical calculations applied to valence and Rydberg excited states of C2H3F. At 7.6 eV the pi-pi* and the 2a"->3s transitions are observed. An analysis is proposed and applied to the mixed fine structure belonging to these transitions. For the pi->pi* transition one single long vibrational progression is observed with hcwe= 95±7 meV (766±56 cm-1) and its adiabatic excitation energy is 6.892 eV (55 588 cm-1). The 2a"->3s transition is characterized by a single short progression with hc e= 167±10 meV (1 350±80 cm-1)starting at 6.974 eV (56 249 cm-1). From the present ab initio calculations these two wavenumbers best correspond to the vibrational modes v9 (CH2 rock in-plane, FCCbend) and v6 (CH2 rock in-plane, CF stretch) calculated at 615 cm-1 in the pi* state and 1 315 cm-1 in the (2A")3s Rydberg state respectively. The C=C stretching could not be excluded. The dense structured spectrum observed between 8.0 eV and 10.5 eV has been analyzed in terms of vibronic transitions to Rydberg states all converging to the C2H3F+(X2A") ionic ground state. An analysis of the associated complex fine structure of the individual Rydberg states has been attempted providing average values of the wavenumbers, e.g., for the (2A")3p Rydberg state hcw9= 60±1 meV (or 484±8 cm-1), hcw7= 151±7 meV (or 1 218±60 cm-1), hcw4= 191±3 meV (or 1 540±24 cm-1). The assignment of hcw= 105±5 meV (or 823±40 cm-1) is discussed. These experimental values are in good agreement with the theoretical predictions for C2H3F+ [R. Locht, B. Leyh, D. Dehareng, K. Hottmann, H. Baumgärtel, Chem.Phys. (in press)]. Above 10.5 eV and up to 25 eV several broad and strong bands are tentatively assigned to transitions to valence (V-V) and/or Rydberg (V-R) states converging to excited ionic states of C2H3F. [less ▲]

The catalytic efficiency of the class D beta-lactamase OXA-10 depends critically on an unusual carboxylated lysine as the general base residue for both the enzyme acylation and deacylation steps of ... [more ▼]

The catalytic efficiency of the class D beta-lactamase OXA-10 depends critically on an unusual carboxylated lysine as the general base residue for both the enzyme acylation and deacylation steps of catalysis. Evidence is presented that the interaction between the indole group of Trp154 and the carboxylated lysine is essential for the stability of the posttranslationally modified Lys70. Substitution of Trp154 by Gly, Ala, or Phe yielded noncarboxylated enzymes which displayed poor catalytic efficiencies and reduced stability when compared to the wild-type OXA-10. The W154H mutant was partially carboxylated. In addition, the maximum values of k(cat) and k(cat)/K(M) were shifted toward pH 7, indicating that the carboxylation state of Lys70 is dependent on the protonation level of the histidine. A comparison of the three-dimensional structures of the different proteins also indicated that the Trp154 mutations did not modify the overall structures of OXA-10 but induced an increased flexibility of the Omega-loop in the active site. Finally, the deacylation-impaired W154A mutant was used to determine the structure of the acyl-enzyme complex with benzylpenicillin. These results indicate a role of the Lys70 carboxylation during the deacylation step and emphasize the importance of Trp154 for the ideal positioning of active site residues leading to an optimum activity. [less ▲]

The peptidoglycan glycosyltransferase (GT) module of class A penicillin-binding proteins (PBPs) and monofunctional GTs catalyze glycan chain elongation of the bacterial cell wall. These enzymes belong to the GT51 family, are characterized by five conserved motifs, and have some fold similarity with the phage lambda lysozyme. In this work, we have systematically modified all the conserved amino acid residues of the GT module of Escherichia coli class A PBP1b by site-directed mutagenesis and determined their importance for the in vivo and in vitro activity and the thermostability of the protein. To get an insight into the GT active site of this paradigm enzyme, a model of PBP1b GT domain was constructed based on the available crystal structures (PDB codes 2OLV and 2OLU). The data show that in addition to the essential glutamate residues Glu233 of motif 1 and Glu290 of motif 3, the residues Phe237 and His240 of motif 1 and Gly264, Thr267, Gln271, and Lys274 of motif 2, all located in the catalytic cavity of the GT domain, are essential for the in vitro enzymatic activity of the PBP1b and for its in vivo functioning. Thus, the first three conserved motifs contain most of the residues that are required for the GT activity of the PBP1b. The residues Asp234, Phe237, His240, Thr267, and Gln271 are proposed to maintain the structure of the active site and the positioning of the catalytic Glu233. [less ▲]

The major allergen Der p1 of the house dust mite Dermatophagoides pteronyssinus is a papain-like cysteine protease (CA1) produced as an inactive precursor and associated with allergic diseases. The ... [more ▼]

The major allergen Der p1 of the house dust mite Dermatophagoides pteronyssinus is a papain-like cysteine protease (CA1) produced as an inactive precursor and associated with allergic diseases. The propeptide of Der p I exhibits a specific fold that makes it unique in the CA1 propeptide family. In this study, we investigated the activation steps involved in the maturation of the recombinant protease Der p 1 expressed in Pichia pastoris and the interaction of the full-length and truncated soluble propepticles with their parent enzyme in terms of activity inhibition and BIAcore interaction analysis. According to our results, the activation of protease Der p 1 is a multistep mechanism that is characterized by at least two intermediates. The propeptide strongly inhibits unglycosylated and glycosylated recombinant Der p 1 (K-D = 7 nM) at neutral pH. This inhibition is pH dependent. It decreases from pH 7 to pH 4 and can be related to conformational changes of the propepticle characterized by an increase of its flexibility and formation of a molten globule state. Our results indicate that activation of the zymogen at pH 4 is a compromise between activity preservation and propeptide unfolding. (c) 2007 Elsevier Ltd. All rights reserved. [less ▲]

in Journal of the American Society for Mass Spectrometry (2007), 18(10), 1827-1834

Gas-phase hydrogen/deuterium exchange of six deprotonated dinucleoticles with CD3OD was performed in the second hexapole of a Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer. To ... [more ▼]

Gas-phase hydrogen/deuterium exchange of six deprotonated dinucleoticles with CD3OD was performed in the second hexapole of a Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer. To complete these experiments, dynamic simulations were carried out to investigate the different conformations adopted by the dinucleotides. In the experimental conditions and in integrating the experimental and theoretical results, H/D exchange was shown to be controlled by hydrogen accessibility and not by the chemical nature of the heteroatom bearing the exchangeable hydrogen. A model including simultaneous H/D exchanges at the experimental time scale was used to reproduce the dinucleotide H/D exchange kinetic plots. The relay mechanism was not relevant for dinucleotides. This allowed the H/D exchange rates to be directly linked to conformations. [less ▲]

The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the ... [more ▼]

The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH2 terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH2 = CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH2 terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide. [less ▲]

The ionization of the four DNA bases is investigated by means of ab initio calculations. Accurate values of the gas-phase vertical and adiabatic ionization potentials (IP) are obtained at the MP2/6-31G(2d ... [more ▼]

The ionization of the four DNA bases is investigated by means of ab initio calculations. Accurate values of the gas-phase vertical and adiabatic ionization potentials (IP) are obtained at the MP2/6-31G(2d(0.8, alpha(d)), p) level of theory. The need of introducing extra polarization to the standard 6-31G(d, p) basis set is demonstrated by test calculations and an optimal value of alpha(d) = 0.1 is obtained. Ionization to electronically excited radical cations is also considered. The low-lying excited states of the cations are characterized for the first time. The topology of the corresponding potential energy surfaces is qualitatively described in terms of the stationary points ( minima and saddle points) located on these surfaces. A conical intersection is characterized for the first time on the ground-state potential energy surface of all cations. It arises from the crossing of the adiabatic surfaces of the ground and first excited state at planar geometries. A nonplanar minimum is observed for the cytosine cation only. The geometry and electronic changes occurring along these surfaces are analyzed, leading to a comparison between the different nucleobase cations. The study of larger ionized systems related to DNA is rendered possible thanks to the optimized medium size basis set proposed in this work, as exemplified by the calculation of the IP of a stacked dimer of guanines. [less ▲]

The triplet Hartree-Fock (HF) instability is investigated through the examples of substituted ethylenes and the small linear conjugated systems butadiene, hexatriene, octatetraene. A statistical analysis ... [more ▼]

The triplet Hartree-Fock (HF) instability is investigated through the examples of substituted ethylenes and the small linear conjugated systems butadiene, hexatriene, octatetraene. A statistical analysis is performed for several conformations of the latters. The second eigenvalue of the instability matrix appears to be able to discriminate the groups of unsaturated compounds. The HF instability is largely influenced by conjugation and mesomeric effects and thus by the geometry. The number of pi electrons is also an important factor. The electronic correlation related to the HF instability is not quantified by the energy difference between the post-HF and HF levels. (c) 2005 Elsevier B.V. All rights reserved. [less ▲]

The threshold photoelectron (TPES) and the photoionization mass spectrometric (PIMS) study of CH3Br in the 8-20 eV photon energy range is presented. The interpretation and assignments are supported by ab ... [more ▼]

The threshold photoelectron (TPES) and the photoionization mass spectrometric (PIMS) study of CH3Br in the 8-20 eV photon energy range is presented. The interpretation and assignments are supported by ab initio calculations. The TPES shows several new discrete features in the Jahn-Teller split ground state X2E(2A'-2A") of CH3Br+. An additional continuous band starts at about 11.8 eV. These observations are both correlated with direct ionization and autoionizing transitions. This is supported by constant ion state (CIS) spectroscopy. A large enhancement of the transitions to the A2A and B2E states is ascribed to important autoionizing contributions. Based on the present calculations, the weak to very weak bands in the 17.5-22.0 eV photon energy range were mainly assigned to 2a1 ionization and to double excitations described essentially by the 2e-24a11 and 1e-12e-14a11 configurations. The photoionization mass spectrometric study allows us to investigate in detail the ionization and dissociation of CH3Br+ leading to CH2+, CH3+, Br+ and CH2Br+ from threshold up to 20 eV photon energy. The experimental data are compared to ab initio dissociation energies. At the onset, the CH3+ and CH2Br+ fragment ion production is correlated with the ground state of CH3Br+ and both fragment ions have to appear through dissociative autoionization from the (3a11/1e1)6s or 5s Rydberg state. This interpretation is supported by the photoabsorption spectrum measured recently in the same photon energy range. At higher energies, beside a likely direct (pre)dissociation of the A2A1 and B2E states of CH3Br+, autoionization also contributes to the fragmentation in all decay channels. Avoided crossings in a manyfold of 2A' states are likely to be involved. This is supported by ab initio calculations. For CH3+ the photoion-pair process is analyzed and detailed assignments are proposed on the basis of our latest VUV photoabsorption spectroscopic data. [less ▲]